What exactly is messed up? The bottleneck was the Comcast/Cogent interlink, which Netflix has now bypassed, which was the entire point of the deal.
The idea that Netflix is paying protection money so that Comcast doesn't do the old "Nice service you got there, it'd be a shame if someone throttled it" (as is implied in the article) is just incorrect. Netflix was buying transit from Cogent. Cogent couldn't deliver the transit that Netflix bought due to conflicts with Comcast. Netflix stops buying transit from Cogent and starts buying transit from Comcast. Comcast delivers all the transit that Netflix buys. Everyone is happy except for Cogent.